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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.seq;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.Iterator;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.symbol.RangeLocation;
import org.biojava.bio.symbol.SymbolList;
/**
* Tests for Serialization
*
* @author Mark Schreiber
* @since 1.3
*/
public class SeqSerializationTest extends TestCase
{
protected Sequence seq;
protected Sequence seq2;
public SeqSerializationTest(String name) {
super(name);
}
protected void setUp() throws Exception {
seq = new SimpleSequence(DNATools.createDNA("aacgtaggttccatgc"),
"fragment1",
"fragment1",
Annotation.EMPTY_ANNOTATION);
Feature.Template sft = new Feature.Template();
sft.type = "test";
sft.source = "test";
sft.annotation = Annotation.EMPTY_ANNOTATION;
sft.location = new RangeLocation(1, 3);
seq.createFeature(sft);
sft.location = new RangeLocation(10, 12);
seq.createFeature(sft);
ByteArrayOutputStream os = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(new BufferedOutputStream(os));
oos.writeObject(seq);
oos.flush();
oos.close();
ObjectInputStream ois = new ObjectInputStream(
new BufferedInputStream(new ByteArrayInputStream(os.toByteArray())));
seq2 = (Sequence)ois.readObject();
}
private boolean compareSymbolList(SymbolList sl1, SymbolList sl2) {
if (sl1.length() != sl2.length()) {
return false;
}
Iterator si1 = sl1.iterator();
Iterator si2 = sl2.iterator();
while (si1.hasNext()) {
if (! (si1.next() == si2.next())) {
return false;
}
}
return true;
}
public void testSymbols()
throws Exception
{
assertTrue(compareSymbolList(seq,seq2));
}
public void testAlphabet()throws Exception{
assertTrue(seq.getAlphabet()==seq2.getAlphabet());
}
public void testFeatures() throws Exception{
assertTrue(seq.countFeatures() == seq2.countFeatures());
}
public void testTokenization(){
assertEquals(seq.seqString(), seq2.seqString());
}
}
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